Cannot update super su binary

I occasionally get a message stating "cannot update supersu binary. This is a problem" (something to that nature). I usually fix this problem by going into philz recovery and fixing root or manually flashing an older version of supersu. However, every time I reboot the phone I get the same "cannot update supersu binary". I am wondering if this could be a recovery issue. Every time I reboot through recovery or just reboot I have to update binary again. Is there a setting on philz that I am unaware of? I recently downloaded twrp manager and cleared cache and dalvik through that and when the phone rebooted I had no binary update issues.

Another thing I was wondering is could this be a Knox problem? I actually tried ota update to 4.3 ( i was rooted in 4.1.2) and it failed. Some time after manually upgrading to 4.3 I received a android security upgrade request. I did not accept the ota update. Is there any way to check if I have knox on my phone? Thank you

One thing I noticed. I dl a previous version of super su in recovery. I will have root access and all my apps that require root will work but there is no super su app. Once I dl supersu from playstore I will not be able to use apps that require root after rebooting

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